Biochimica et Biophysica Acta 1778 (2008) 1757–1771 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbamem Review ATP-binding cassette transporters in Escherichia coli Anastassiia Moussatova, Christian Kandt, Megan L. O'Mara, D. Peter Tieleman ⁎ Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4 article info abstract Article history: ATP-binding cassette (ABC) transporters are integral membrane proteins that actively transport molecules Received 9 January 2008 across cell membranes. In Escherichia coli they consist primarily of import systems that involve in addition to Received in revised form 10 June 2008 the ABC transporter itself a substrate binding protein and outer membrane receptors or porins, and a number Accepted 12 June 2008 of transporters with varied functions. Recent crystal structures of a number of ATPase domains, substrate Available online 18 June 2008 binding proteins, and full-length transporters have given new insight in the molecular basis of transport. fi Keywords: Bioinformatics approaches allow an approximate identi cation of all ABC transporters in E. coli and their ABC transporter relation to other known transporters. Computational approaches involving modeling and simulation are Homology beginning to yield insight into the dynamics of the transporters. We summarize the function of the known Periplasmic binding protein ABC transporters in E. coli and mechanistic insights from structural and computational studies. BtuCD © 2008 Elsevier B.V. All rights reserved. Simulation Importer P-glycoprotein Contents 1. Introduction .............................................................. 1757 2. Structure of ABC transporters ...................................................... 1758 2.1. General structure of ABC transporters............................................... 1758 2.2. Bacterial ABC transporters .................................................... 1760 3. ABC transporters in E. coli ....................................................... 1762 4. Structural data on E. coli ABC transporters ................................................ 1762 4.1. Structure of nucleotide binding domains ............................................. 1763 4.2. Structures of full ABC transporters ................................................ 1764 5. Computational findings ......................................................... 1766 5.1. Structure prediction ....................................................... 1766 5.2. Complex modeling ....................................................... 1766 5.3. Protein dynamics ........................................................ 1766 5.3.1. Substrate binding proteins ................................................ 1766 5.3.2. Nucleotide binding domains ............................................... 1767 5.3.3. Full-length ABC transporters............................................... 1767 6. Conclusion............................................................... 1768 Acknowledgements ............................................................. 1768 References ................................................................. 1768 1. Introduction hydrolysis of ATP to ADP. This ubiquitous class of transporters is present in virtually all living organisms and accounts for large variety ATP-binding cassette (ABC) transporters are integral membrane of biological processes. It should be noted that the ABC domain can proteins that actively transport molecules across the lipid membrane also be found in proteins that may couple ATP hydrolysis to functions against a concentration gradient, using the energy derived from the other than transport, for instance in DNA repair [1,2]. However, while such proteins can contribute to our understanding of catalytic ⁎ Corresponding author. processes, the present review will be focused only on the ABC E-mail address: [email protected] (D.P. Tieleman). transporter family. 0005-2736/$ – see front matter © 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.bbamem.2008.06.009 1758 A. Moussatova et al. / Biochimica et Biophysica Acta 1778 (2008) 1757–1771 Specialized ABC transporter types transport a diverse range of substrates, ranging from small molecules such as ions, sugars or amino acids to larger compounds such as antibiotics, drugs, lipids and oligopeptides. ABC transporters take part in the uptake of nutrients or secretion of toxins in bacteria, as well as confer multidrug resistance in cancer or bacterial cells by pumping diverse anti-cancer drugs and antibiotics into the extracellular spaces. The ABC transporters are also medically relevant as some of their mutations have been implicated in genetic disorders such as cystic fibrosis. These proteins constitute a very ancient family of transporters, believed to date back in evolutionary time more than 3 billion years [3]. Phylogenetic evidence supports the idea that the ABC transpor- ter family diversified before bacteria, archea and eukaryotes diverged on separate evolutionary paths [4], thus many human ABC transporters have bacterial homologues in organisms such as Escherichia coli (E. coli). E. coli is a Gram-negative bacillus native to the intestinal flora of many animals, including humans [5]. It is a facultative anaerobe which survives when released to the natural environment and can often be found in soil or as a contaminant in untreated water. The diversity of the natural reservoir and the vectorial transfer of plasmid genes means that E. coli as a species is not well delineated, encompassing a wide variety of biotypes or strains. In addition to chromosomal and plasmid genes encoding antibiotic resistance, biochemical adaptations or other virulence factors, individual strains also express various antigenic lipoproteins or glycolipoproteins anchored in the peptido- glycan cell wall. As these antigenic surface proteins vary from strain to strain, differentiation of E. coli species is based on antigen expression [6]. The K-12 strain, a non-virulent strain lacking the O and K antigens [5], is the most widely used laboratory strain and is often referred to as the standard E. coli culture. In 1997, the complete genome of E. coli K-12 serotype was sequenced [7]. The largest single family of proteins in the E. coli K- 12 genome is the ABC transporter family, comprising 5% of the total genome together with all transport related components [1].Ina recent book, the classification of ABC transporters in families in Gram- negative bacteria was reviewed [8]. Here we focus on ABC transporters from E. coli, their roles, and the available structural data from both experiment and computation. It is expected that the information collected about E. coli ABC transporters would provide a good base for study and comparison of structural and functional aspects in the homologous proteins from other organisms. 2. Structure of ABC transporters 2.1. General structure of ABC transporters As illustrated in Fig. 1a all ABC transporters share a common basic structure regardless of their function as importer or exporter or the substances transported. ABC transporters are composed of two transmembrane domains (TMDs) which are the integral membrane proteins and two nucleotide binding domains (NBDs), water soluble proteins associated with the TMDs on one side of the membrane (Fig. 1a). The TMD parts of the transporter form the transport channel and consist of several membrane-spanning alpha-helices presenting considerable structural variability among ABC transporters. The number of transmembrane helices also varies between 8–20 for Fig. 1. General ABC transporter architecture (a) comprises two transmembrane domains importers and 12 for exporters [9]. (TMD, blue) and two nucleotide binding domains (NBD, green). Some transporters receive their substrate (red) from the bilayer, some from the aqueous phase. In case of In contrast, the NBD parts are highly conserved among the ABC the latter specialized substrate binding proteins (yellow) can deliver the substrate to the protein family presenting the characteristic Walker A and B motifs transporter. This is typically found in Gram-negative bacteria. BtuCD (b) consists of four found in all ATP-binding proteins as well as a signature motif which is single polypeptide chains and receives its vitamin B12 substrate via the substrate specific to the ABC transporter family. The NBDs are the engines of an binding protein BtuF. Sav1866 (c) comprises two polypeptide chains and binds its ABC transporter as they bind and hydrolyse ATP, powering transport. substrate from the bilayer. BtuCD and Sav1866 represent two types of TMD organization with the polypeptide chain crossing the bilayer ten (b) or six times (c). (b) has been ATP binding induces conformational changes in NBDs, forcing them adapted from [67]. into closer contact and forming the characteristic nucleotide sandwich A. Moussatova et al. / Biochimica et Biophysica Acta 1778 (2008) 1757–1771 1759 Table 1 Functional E. coli ABC transporters, number of components, biological function and analogous role in other bacteria Transporter Components Substrate Biological function Reference Prokaryotic-like transporters Als AlsB (BP), AlsC (TM), AlsA (NB) Allose, ribose Monosaccharide importer [84] Ara AraF (BP), AraH (TM), AraG (NB) L-arabinose, fructose, xylose Monosaccharide porter [85] Arg ArgT (BP), HisQ (TMD), HisM (TMD), L-lysine, L-arginine, L-ornithine Polar amino acid transporter